An EM algorithm based on an internal list for estimating haplotype distributions of rare variants from pooled genotype data.

ABSTRACT:

Background

Pooling is a cost effective way to collect data for genetic association studies, particularly for rare genetic variants. It is of interest to estimate the haplotype frequencies, which contain more information than single locus statistics. By viewing the pooled genotype data as incomplete data, the expectation-maximization (EM) algorithm is the natural algorithm to use, but it is computationally intensive. A recent proposal to reduce the computational burden is to make use of database information to form a list of frequently occurring haplotypes, and to restrict the haplotypes to come from this list only in implementing the EM algorithm. There is, however, the danger of using an incorrect list, and there may not be enough database information to form a list externally in

SUBMITTER: Kuk AY 

PROVIDER: S-EPMC3847674 | biostudies-literature | 2013 Sep

REPOSITORIES: biostudies-literature